The Weinstock laboratory uses a variety of in vitro and in vivo techniques to identify novel oncogene alterations directly from tumor specimens and elucidate mechanisms of aberrant DNA repair within malignant and nonmalignant stem cells.

Functional Oncogene Identification. Systematic analyses to determine the functional sequelae of somatic mutations from tumor samples have proven cumbersome and low-yield. We developed an alternate approach that uses retroviral cDNA libraries to specifically characterize functional alterations. In this system, patient-derived libraries are transduced into cells to identify oncogene alterations that confer a distinct phenotype on the recipient cell, such as differentiation arrest or growth factor independence. With this approach, cryptic mutations, translocations and other rearrangements with functional significance can be identified. This approach is used to complement next-generation sequencing and traditional gene discovery approaches.

We are currently assaying retroviral cDNA libraries from a panel of hematologic malignancies with unclear genetics. Oncogenes identified by the screen are pursued with the goal of translating these discoveries into novel cancer therapies, as outlined below.

CRLF2 in B-cell acute lymphoblastic leukemia (B-ALL). Our initial efforts identified CRLF2, a previously obscure cytokine receptor, as an essential oncogene in 15% of adult and high-risk pediatric B-ALL that lack other characteristic rearrangements, and 60% of B-ALL in children with Down Syndrome. In these cases, overexpression uniformly results from genomic rearrangements that place full-length CRLF2 under alternate transcriptional control. Outcomes from B-ALL that overexpress CRLF2 are dismal, with a 4-year overall survival among adults of 0% compared with 60% for non-overexpressing cases.

B-ALLs that overexpress CRLF2 frequently harbor gain-of-function mutations either within CRLF2 itself or in the kinase JAK2. JAK2 enzymatic activity requires interaction with a cytokine receptor, which is believed to serve as a scaffold for JAK2 and its substrates. Strikingly, all reported B-ALLs that harbor JAK2 mutations also overexpress CRLF2, suggesting that CRLF2 is the essential scaffold for mutant JAK2 activity in B-ALL.

The availability of JAK inhibitors, which are now in clinical trials for the treatment of myeloproliferative disorders, offers an extraordinary opportunity to rapidly translate this discovery into a directed therapy for patients with CRLF2-overexpressing B-ALL. We are now addressing the mechanisms of CRLF2 signaling in B-ALL, first by defining its essential components and then by assaying small molecule and monoclonal antibody pharmacologics that target this novel pathway in primary human xenografts and genetically engineered mouse models.

DNA Repair in Tumor and Normal Stem Cells. Despite their extraordinary potential, little is known about the nature and determinants of DNA double-strand break (DSB) repair in pluripotent human cells, both human embryonic stem cells (hESCs) and induced pluripotent cells (iPSCs). To assay DSB repair in these cells, we use targeted reporters and zinc finger nucleases capable of assaying repair at precisely introduced chromosomal breaks. With this approach, we have determined that DSB repair in hESCs differs from repair in many cell lines, with a preference for highly precise NHEJ over homologous repair. In addition, we identified a novel interaction between the base excision repair protein PARP1 and the anti-apoptotic BCL2 that suppresses DNA repair and necrotic cell death within tumor cells. Our current efforts utilize chemical genetics and RNAi to modulate DNA repair in stem cells, identify factors that regulate interchromosomal repair events, and augment gene modification strategies.